Nested replies are definitely better as a way of consuming a post and its comments once and then never thinking about it again. For an asynchronous discussion between several people they get unwieldy after a few rounds of replying. They also make it harder to coherently reference points made cross-tree. That plus algorithmic ranking gives a constant feeling of "gotta refresh to see if there's new stuff" that serves a site like Reddit well, but it makes it much harder to have a longer discussion with more back and forth.

Having recently started participating in a community where most useful discussions are on a PhpBB forum, going back to linear posting was actually refreshing. It's easy to stay on top of because you can check in once a day or so and see just the conversations that have updates since you've last checked them. Threads being sorted by most recently updated means you focus on where there's active discussion. And once you've read those things there's no reason to stick around. "That's it! Get back to doing something useful."

Obviously, this doesn't really scale to a community the size of reddit, but I think it's really pleasant for medium-sized communities.